-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
- * \r
- * This file is part of Jalview.\r
- * \r
- * Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
- * PURPOSE. See the GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
- */\r
-package jalview.gui;\r
-\r
-import java.util.*;\r
-import java.awt.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-\r
-import java.awt.event.*;\r
-import java.io.*;\r
-\r
-import jalview.jbgui.GStructureViewer;\r
-import jalview.api.SequenceStructureBinding;\r
-import jalview.bin.Cache;\r
-import jalview.datamodel.*;\r
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;\r
-import jalview.datamodel.PDBEntry;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
-import jalview.util.MessageManager;\r
-import jalview.util.Platform;\r
-\r
-public class AppJmol extends GStructureViewer implements Runnable,\r
- SequenceStructureBinding, ViewSetProvider\r
-\r
-{\r
- AppJmolBinding jmb;\r
-\r
- JPanel scriptWindow;\r
-\r
- JSplitPane splitPane;\r
-\r
- RenderPanel renderPanel;\r
-\r
- AlignmentPanel ap;\r
-\r
- Vector atomsPicked = new Vector();\r
-\r
- private boolean addingStructures = false;\r
-\r
- /**\r
- * \r
- * @param file\r
- * @param id\r
- * @param seq\r
- * @param ap\r
- * @param loadStatus\r
- * @param bounds\r
- * @deprecated defaults to AppJmol(String[] files, ... , viewid);\r
- */\r
- public AppJmol(String file, String id, SequenceI[] seq,\r
- AlignmentPanel ap, String loadStatus, Rectangle bounds)\r
- {\r
- this(file, id, seq, ap, loadStatus, bounds, null);\r
- }\r
-\r
- /**\r
- * @deprecated\r
- */\r
- public AppJmol(String file, String id, SequenceI[] seq,\r
- AlignmentPanel ap, String loadStatus, Rectangle bounds,\r
- String viewid)\r
- {\r
- this(new String[]\r
- { file }, new String[]\r
- { id }, new SequenceI[][]\r
- { seq }, ap, true, true, false, loadStatus, bounds, viewid);\r
- }\r
-\r
- ViewSelectionMenu seqColourBy;\r
-\r
- /**\r
- * \r
- * @param files\r
- * @param ids\r
- * @param seqs\r
- * @param ap\r
- * @param usetoColour\r
- * - add the alignment panel to the list used for colouring these\r
- * structures\r
- * @param useToAlign\r
- * - add the alignment panel to the list used for aligning these\r
- * structures\r
- * @param leaveColouringToJmol\r
- * - do not update the colours from any other source. Jmol is\r
- * handling them\r
- * @param loadStatus\r
- * @param bounds\r
- * @param viewid\r
- */\r
- public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,\r
- AlignmentPanel ap, boolean usetoColour, boolean useToAlign,\r
- boolean leaveColouringToJmol, String loadStatus,\r
- Rectangle bounds, String viewid)\r
- {\r
- PDBEntry[] pdbentrys = new PDBEntry[files.length];\r
- for (int i = 0; i < pdbentrys.length; i++)\r
- {\r
- PDBEntry pdbentry = new PDBEntry();\r
- pdbentry.setFile(files[i]);\r
- pdbentry.setId(ids[i]);\r
- pdbentrys[i] = pdbentry;\r
- }\r
- // / TODO: check if protocol is needed to be set, and if chains are\r
- // autodiscovered.\r
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),\r
- pdbentrys, seqs, null, null);\r
-\r
- jmb.setLoadingFromArchive(true);\r
- addAlignmentPanel(ap);\r
- if (useToAlign)\r
- {\r
- useAlignmentPanelForSuperposition(ap);\r
- }\r
- if (leaveColouringToJmol || !usetoColour)\r
- {\r
- jmb.setColourBySequence(false);\r
- seqColour.setSelected(false);\r
- jmolColour.setSelected(true);\r
- }\r
- if (usetoColour)\r
- {\r
- useAlignmentPanelForColourbyseq(ap);\r
- jmb.setColourBySequence(true);\r
- seqColour.setSelected(true);\r
- jmolColour.setSelected(false);\r
- }\r
- this.setBounds(bounds);\r
- initMenus();\r
- viewId = viewid;\r
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",\r
- // bounds.width,bounds.height);\r
-\r
- this.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
- {\r
- closeViewer();\r
- }\r
- });\r
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!\r
-\r
- }\r
-\r
- private void initMenus()\r
- {\r
- seqColour.setSelected(jmb.isColourBySequence());\r
- jmolColour.setSelected(!jmb.isColourBySequence());\r
- if (_colourwith == null)\r
- {\r
- _colourwith = new Vector<AlignmentPanel>();\r
- }\r
- if (_alignwith == null)\r
- {\r
- _alignwith = new Vector<AlignmentPanel>();\r
- }\r
-\r
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,\r
- new ItemListener()\r
- {\r
-\r
- @Override\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- if (!seqColour.isSelected())\r
- {\r
- seqColour.doClick();\r
- }\r
- else\r
- {\r
- // update the jmol display now.\r
- seqColour_actionPerformed(null);\r
- }\r
- }\r
- });\r
- viewMenu.add(seqColourBy);\r
- final ItemListener handler;\r
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,\r
- _alignwith, handler = new ItemListener()\r
- {\r
-\r
- @Override\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- alignStructs.setEnabled(_alignwith.size() > 0);\r
- alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));\r
- }\r
- });\r
- handler.itemStateChanged(null);\r
- jmolActionMenu.add(alpanels);\r
- jmolActionMenu.addMenuListener(new MenuListener()\r
- {\r
-\r
- @Override\r
- public void menuSelected(MenuEvent e)\r
- {\r
- handler.itemStateChanged(null);\r
- }\r
-\r
- @Override\r
- public void menuDeselected(MenuEvent e)\r
- {\r
- // TODO Auto-generated method stub\r
-\r
- }\r
-\r
- @Override\r
- public void menuCanceled(MenuEvent e)\r
- {\r
- // TODO Auto-generated method stub\r
-\r
- }\r
- });\r
- }\r
-\r
- IProgressIndicator progressBar = null;\r
-\r
- /**\r
- * add a single PDB structure to a new or existing Jmol view\r
- * \r
- * @param pdbentry\r
- * @param seq\r
- * @param chains\r
- * @param ap\r
- */\r
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,\r
- final AlignmentPanel ap)\r
- {\r
- progressBar = ap.alignFrame;\r
- // ////////////////////////////////\r
- // Is the pdb file already loaded?\r
- String alreadyMapped = ap.getStructureSelectionManager()\r
- .alreadyMappedToFile(pdbentry.getId());\r
-\r
- if (alreadyMapped != null)\r
- {\r
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),\r
- MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),\r
- JOptionPane.YES_NO_OPTION);\r
-\r
- if (option == JOptionPane.YES_OPTION)\r
- {\r
- // TODO : Fix multiple seq to one chain issue here.\r
- ap.getStructureSelectionManager().setMapping(seq, chains,\r
- alreadyMapped, AppletFormatAdapter.FILE);\r
- if (ap.seqPanel.seqCanvas.fr != null)\r
- {\r
- ap.seqPanel.seqCanvas.fr.featuresAdded();\r
- ap.paintAlignment(true);\r
- }\r
-\r
- // Now this AppJmol is mapped to new sequences. We must add them to\r
- // the exisiting array\r
- JInternalFrame[] frames = Desktop.instance.getAllFrames();\r
-\r
- for (int i = 0; i < frames.length; i++)\r
- {\r
- if (frames[i] instanceof AppJmol)\r
- {\r
- final AppJmol topJmol = ((AppJmol) frames[i]);\r
- // JBPNOTE: this looks like a binding routine, rather than a gui\r
- // routine\r
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)\r
- {\r
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))\r
- {\r
- topJmol.jmb.addSequence(pe, seq);\r
- topJmol.addAlignmentPanel(ap);\r
- // add it to the set used for colouring\r
- topJmol.useAlignmentPanelForColourbyseq(ap);\r
- topJmol.buildJmolActionMenu();\r
- ap.getStructureSelectionManager()\r
- .sequenceColoursChanged(ap);\r
- break;\r
- }\r
- }\r
- }\r
- }\r
-\r
- return;\r
- }\r
- }\r
- // /////////////////////////////////\r
- // Check if there are other Jmol views involving this alignment\r
- // and prompt user about adding this molecule to one of them\r
- Vector existingViews = getJmolsFor(ap);\r
- if (existingViews.size() > 0)\r
- {\r
- Enumeration jm = existingViews.elements();\r
- while (jm.hasMoreElements())\r
- {\r
- AppJmol topJmol = (AppJmol) jm.nextElement();\r
- // TODO: highlight topJmol in view somehow\r
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),\r
- MessageManager.getString("label.align_to_existing_structure_view"),\r
- JOptionPane.YES_NO_OPTION);\r
- if (option == JOptionPane.YES_OPTION)\r
- {\r
- topJmol.useAlignmentPanelForSuperposition(ap);\r
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);\r
- return;\r
- }\r
- }\r
- }\r
- // /////////////////////////////////\r
- openNewJmol(ap, new PDBEntry[]\r
- { pdbentry }, new SequenceI[][]\r
- { seq });\r
- }\r
-\r
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,\r
- SequenceI[][] seqs)\r
- {\r
- progressBar = ap.alignFrame;\r
- jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),\r
- pdbentrys, seqs, null, null);\r
- addAlignmentPanel(ap);\r
- useAlignmentPanelForColourbyseq(ap);\r
- if (pdbentrys.length > 1)\r
- {\r
- alignAddedStructures = true;\r
- useAlignmentPanelForSuperposition(ap);\r
- }\r
- jmb.setColourBySequence(true);\r
- setSize(400, 400); // probably should be a configurable/dynamic default here\r
- initMenus();\r
- worker = null;\r
- {\r
- addingStructures = false;\r
- worker = new Thread(this);\r
- worker.start();\r
- }\r
- this.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)\r
- {\r
- closeViewer();\r
- }\r
- });\r
-\r
- }\r
-\r
- /**\r
- * create a new Jmol containing several structures superimposed using the\r
- * given alignPanel.\r
- * \r
- * @param ap\r
- * @param pe\r
- * @param seqs\r
- */\r
- public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)\r
- {\r
- openNewJmol(ap, pe, seqs);\r
- }\r
-\r
- /**\r
- * list of sequenceSet ids associated with the view\r
- */\r
- ArrayList<String> _aps = new ArrayList();\r
-\r
- public AlignmentPanel[] getAllAlignmentPanels()\r
- {\r
- AlignmentPanel[] t, list = new AlignmentPanel[0];\r
- for (String setid : _aps)\r
- {\r
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);\r
- if (panels != null)\r
- {\r
- t = new AlignmentPanel[list.length + panels.length];\r
- System.arraycopy(list, 0, t, 0, list.length);\r
- System.arraycopy(panels, 0, t, list.length, panels.length);\r
- list = t;\r
- }\r
- }\r
-\r
- return list;\r
- }\r
-\r
- /**\r
- * list of alignment panels to use for superposition\r
- */\r
- Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();\r
-\r
- /**\r
- * list of alignment panels that are used for colouring structures by aligned\r
- * sequences\r
- */\r
- Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();\r
-\r
- /**\r
- * set the primary alignmentPanel reference and add another alignPanel to the\r
- * list of ones to use for colouring and aligning\r
- * \r
- * @param nap\r
- */\r
- public void addAlignmentPanel(AlignmentPanel nap)\r
- {\r
- if (ap == null)\r
- {\r
- ap = nap;\r
- }\r
- if (!_aps.contains(nap.av.getSequenceSetId()))\r
- {\r
- _aps.add(nap.av.getSequenceSetId());\r
- }\r
- }\r
-\r
- /**\r
- * remove any references held to the given alignment panel\r
- * \r
- * @param nap\r
- */\r
- public void removeAlignmentPanel(AlignmentPanel nap)\r
- {\r
- try\r
- {\r
- _alignwith.remove(nap);\r
- _colourwith.remove(nap);\r
- if (ap == nap)\r
- {\r
- ap = null;\r
- for (AlignmentPanel aps : getAllAlignmentPanels())\r
- {\r
- if (aps != nap)\r
- {\r
- ap = aps;\r
- break;\r
- }\r
- }\r
- }\r
- } catch (Exception ex)\r
- {\r
- }\r
- if (ap != null)\r
- {\r
- buildJmolActionMenu();\r
- }\r
- }\r
-\r
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)\r
- {\r
- addAlignmentPanel(nap);\r
- if (!_alignwith.contains(nap))\r
- {\r
- _alignwith.add(nap);\r
- }\r
- }\r
-\r
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)\r
- {\r
- if (_alignwith.contains(nap))\r
- {\r
- _alignwith.remove(nap);\r
- }\r
- }\r
-\r
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,\r
- boolean enableColourBySeq)\r
- {\r
- useAlignmentPanelForColourbyseq(nap);\r
- jmb.setColourBySequence(enableColourBySeq);\r
- seqColour.setSelected(enableColourBySeq);\r
- jmolColour.setSelected(!enableColourBySeq);\r
- }\r
-\r
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)\r
- {\r
- addAlignmentPanel(nap);\r
- if (!_colourwith.contains(nap))\r
- {\r
- _colourwith.add(nap);\r
- }\r
- }\r
-\r
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)\r
- {\r
- if (_colourwith.contains(nap))\r
- {\r
- _colourwith.remove(nap);\r
- }\r
- }\r
-\r
- /**\r
- * pdb retrieval thread.\r
- */\r
- private Thread worker = null;\r
-\r
- /**\r
- * add a new structure (with associated sequences and chains) to this viewer,\r
- * retrieving it if necessary first.\r
- * \r
- * @param pdbentry\r
- * @param seq\r
- * @param chains\r
- * @param alignFrame\r
- * @param align\r
- * if true, new structure(s) will be align using associated alignment\r
- */\r
- private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,\r
- final String[] chains, final boolean b,\r
- final IProgressIndicator alignFrame)\r
- {\r
- if (pdbentry.getFile() == null)\r
- {\r
- if (worker != null && worker.isAlive())\r
- {\r
- // a retrieval is in progress, wait around and add ourselves to the\r
- // queue.\r
- new Thread(new Runnable()\r
- {\r
- public void run()\r
- {\r
- while (worker != null && worker.isAlive() && _started)\r
- {\r
- try\r
- {\r
- Thread.sleep(100 + ((int) Math.random() * 100));\r
-\r
- } catch (Exception e)\r
- {\r
- }\r
-\r
- }\r
- // and call ourselves again.\r
- addStructure(pdbentry, seq, chains, b, alignFrame);\r
- }\r
- }).start();\r
- return;\r
- }\r
- }\r
- // otherwise, start adding the structure.\r
- jmb.addSequenceAndChain(new PDBEntry[]\r
- { pdbentry }, new SequenceI[][]\r
- { seq }, new String[][]\r
- { chains });\r
- addingStructures = true;\r
- _started = false;\r
- alignAddedStructures = b;\r
- progressBar = alignFrame; // visual indication happens on caller frame.\r
- (worker = new Thread(this)).start();\r
- return;\r
- }\r
-\r
- private Vector getJmolsFor(AlignmentPanel ap2)\r
- {\r
- Vector otherJmols = new Vector();\r
- // Now this AppJmol is mapped to new sequences. We must add them to\r
- // the exisiting array\r
- JInternalFrame[] frames = Desktop.instance.getAllFrames();\r
-\r
- for (int i = 0; i < frames.length; i++)\r
- {\r
- if (frames[i] instanceof AppJmol)\r
- {\r
- AppJmol topJmol = ((AppJmol) frames[i]);\r
- if (topJmol.isLinkedWith(ap2))\r
- {\r
- otherJmols.addElement(topJmol);\r
- }\r
- }\r
- }\r
- return otherJmols;\r
- }\r
-\r
- void initJmol(String command)\r
- {\r
- jmb.setFinishedInit(false);\r
- renderPanel = new RenderPanel();\r
- // TODO: consider waiting until the structure/view is fully loaded before\r
- // displaying\r
- this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);\r
- jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),\r
- getBounds().width, getBounds().height);\r
- if (scriptWindow == null)\r
- {\r
- BorderLayout bl = new BorderLayout();\r
- bl.setHgap(0);\r
- bl.setVgap(0);\r
- scriptWindow = new JPanel(bl);\r
- scriptWindow.setVisible(false);\r
- }\r
- ;\r
- jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,\r
- null);\r
- jmb.newJmolPopup(true, "Jmol", true);\r
- if (command == null)\r
- {\r
- command = "";\r
- }\r
- jmb.evalStateCommand(command);\r
- jmb.setFinishedInit(true);\r
- }\r
-\r
- void setChainMenuItems(Vector chains)\r
- {\r
- chainMenu.removeAll();\r
- if (chains == null)\r
- {\r
- return;\r
- }\r
- JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));\r
- menuItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- allChainsSelected = true;\r
- for (int i = 0; i < chainMenu.getItemCount(); i++)\r
- {\r
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);\r
- }\r
- centerViewer();\r
- allChainsSelected = false;\r
- }\r
- });\r
-\r
- chainMenu.add(menuItem);\r
-\r
- for (int c = 0; c < chains.size(); c++)\r
- {\r
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);\r
- menuItem.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent evt)\r
- {\r
- if (!allChainsSelected)\r
- centerViewer();\r
- }\r
- });\r
-\r
- chainMenu.add(menuItem);\r
- }\r
- }\r
-\r
- boolean allChainsSelected = false;\r
-\r
- private boolean alignAddedStructures = false;\r
-\r
- void centerViewer()\r
- {\r
- Vector toshow = new Vector();\r
- String lbl;\r
- int mlength, p, mnum;\r
- for (int i = 0; i < chainMenu.getItemCount(); i++)\r
- {\r
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)\r
- {\r
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);\r
- if (item.isSelected())\r
- {\r
- toshow.addElement(item.getText());\r
- }\r
- }\r
- }\r
- jmb.centerViewer(toshow);\r
- }\r
-\r
- void closeViewer()\r
- {\r
- jmb.closeViewer();\r
- ap = null;\r
- _aps.clear();\r
- _alignwith.clear();\r
- _colourwith.clear();\r
- // TODO: check for memory leaks where instance isn't finalised because jmb\r
- // holds a reference to the window\r
- jmb = null;\r
- }\r
-\r
- /**\r
- * state flag for PDB retrieval thread\r
- */\r
- private boolean _started = false;\r
-\r
- public void run()\r
- {\r
- _started = true;\r
- String pdbid = "";\r
- // todo - record which pdbids were successfuly imported.\r
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();\r
- try\r
- {\r
- String[] curfiles = jmb.getPdbFile(); // files currently in viewer\r
- // TODO: replace with reference fetching/transfer code (validate PDBentry\r
- // as a DBRef?)\r
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();\r
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)\r
- {\r
- String file = jmb.pdbentry[pi].getFile();\r
- if (file == null)\r
- {\r
- // retrieve the pdb and store it locally\r
- AlignmentI pdbseq = null;\r
- pdbid = jmb.pdbentry[pi].getId();\r
- long hdl = pdbid.hashCode() - System.currentTimeMillis();\r
- if (progressBar != null)\r
- {\r
- progressBar.setProgressBar("Fetching PDB " + pdbid, hdl);\r
- }\r
- try\r
- {\r
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]\r
- .getId());\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- errormsgs.append("'" + pdbid + "'");\r
- }\r
- if (progressBar != null)\r
- {\r
- progressBar.setProgressBar("Finished.", hdl);\r
- }\r
- if (pdbseq != null)\r
- {\r
- // just transfer the file name from the first sequence's first\r
- // PDBEntry\r
- file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()\r
- .elementAt(0)).getFile()).getAbsolutePath();\r
- jmb.pdbentry[pi].setFile(file);\r
-\r
- files.append(" \"" + Platform.escapeString(file) + "\"");\r
- }\r
- else\r
- {\r
- errormsgs.append("'" + pdbid + "' ");\r
- }\r
- }\r
- else\r
- {\r
- if (curfiles != null && curfiles.length > 0)\r
- {\r
- addingStructures = true; // already files loaded.\r
- for (int c = 0; c < curfiles.length; c++)\r
- {\r
- if (curfiles[c].equals(file))\r
- {\r
- file = null;\r
- break;\r
- }\r
- }\r
- }\r
- if (file != null)\r
- {\r
- files.append(" \"" + Platform.escapeString(file) + "\"");\r
- }\r
- }\r
- }\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid\r
- + "'");\r
- }\r
- if (errormsgs.length() > 0)\r
- {\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),\r
- MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);\r
-\r
- }\r
- long lastnotify = jmb.getLoadNotifiesHandled();\r
- if (files.length() > 0)\r
- {\r
- if (!addingStructures)\r
- {\r
-\r
- try\r
- {\r
- initJmol("load FILES " + files.toString());\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);\r
- Cache.log.debug("File locations are " + files);\r
- } catch (Exception ex)\r
- {\r
- Cache.log.error("Couldn't open Jmol viewer!", ex);\r
- }\r
- }\r
- else\r
- {\r
- StringBuffer cmd = new StringBuffer();\r
- cmd.append("loadingJalviewdata=true\nload APPEND ");\r
- cmd.append(files.toString());\r
- cmd.append("\nloadingJalviewdata=null");\r
- final String command = cmd.toString();\r
- cmd = null;\r
- lastnotify = jmb.getLoadNotifiesHandled();\r
-\r
- try\r
- {\r
- jmb.evalStateCommand(command);\r
- } catch (OutOfMemoryError oomerror)\r
- {\r
- new OOMWarning(\r
- "When trying to add structures to the Jmol viewer!",\r
- oomerror);\r
- Cache.log.debug("File locations are " + files);\r
- } catch (Exception ex)\r
- {\r
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);\r
- }\r
- }\r
-\r
- // need to wait around until script has finished\r
- while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()\r
- : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))\r
- {\r
- try\r
- {\r
- Cache.log.debug("Waiting around for jmb notify.");\r
- Thread.sleep(35);\r
- } catch (Exception e)\r
- {\r
- }\r
- }\r
- // refresh the sequence colours for the new structure(s)\r
- for (AlignmentPanel ap : _colourwith)\r
- {\r
- jmb.updateColours(ap);\r
- }\r
- // do superposition if asked to\r
- if (alignAddedStructures)\r
- {\r
- javax.swing.SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- alignStructs_withAllAlignPanels();\r
- // jmb.superposeStructures(ap.av.getAlignment(), -1, null);\r
- }\r
- });\r
- alignAddedStructures = false;\r
- }\r
- addingStructures = false;\r
-\r
- }\r
- _started = false;\r
- worker = null;\r
- }\r
-\r
- public void pdbFile_actionPerformed(ActionEvent actionEvent)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(\r
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save PDB File");\r
- chooser.setToolTipText(MessageManager.getString("action.save"));\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- try\r
- {\r
- // TODO: cope with multiple PDB files in view\r
- BufferedReader in = new BufferedReader(new FileReader(\r
- jmb.getPdbFile()[0]));\r
- File outFile = chooser.getSelectedFile();\r
-\r
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
- String data;\r
- while ((data = in.readLine()) != null)\r
- {\r
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))\r
- {\r
- out.println(data);\r
- }\r
- }\r
- out.close();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- public void viewMapping_actionPerformed(ActionEvent actionEvent)\r
- {\r
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
- try\r
- {\r
- for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++)\r
- {\r
- cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile()));\r
- cap.appendText("\n");\r
- }\r
- } catch (OutOfMemoryError e)\r
- {\r
- new OOMWarning(\r
- "composing sequence-structure alignments for display in text box.",\r
- e);\r
- cap.dispose();\r
- return;\r
- }\r
- jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),\r
- 550, 600);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void eps_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.EPS);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- * \r
- * @param e\r
- * DOCUMENT ME!\r
- */\r
- public void png_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.PNG);\r
- }\r
-\r
- void makePDBImage(int type)\r
- {\r
- int width = getWidth();\r
- int height = getHeight();\r
-\r
- jalview.util.ImageMaker im;\r
-\r
- if (type == jalview.util.ImageMaker.PNG)\r
- {\r
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,\r
- "Make PNG image from view", width, height, null, null);\r
- }\r
- else\r
- {\r
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,\r
- "Make EPS file from view", width, height, null,\r
- this.getTitle());\r
- }\r
-\r
- if (im.getGraphics() != null)\r
- {\r
- Rectangle rect = new Rectangle(width, height);\r
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);\r
- im.writeImage();\r
- }\r
- }\r
-\r
- public void jmolColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- if (jmolColour.isSelected())\r
- {\r
- // disable automatic sequence colouring.\r
- jmb.setColourBySequence(false);\r
- }\r
- }\r
-\r
- public void seqColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- jmb.setColourBySequence(seqColour.isSelected());\r
- if (_colourwith == null)\r
- {\r
- _colourwith = new Vector<AlignmentPanel>();\r
- }\r
- if (jmb.isColourBySequence())\r
- {\r
- if (!jmb.isLoadingFromArchive())\r
- {\r
- if (_colourwith.size() == 0 && ap != null)\r
- {\r
- // Make the currently displayed alignment panel the associated view\r
- _colourwith.add(ap.alignFrame.alignPanel);\r
- }\r
- }\r
- // Set the colour using the current view for the associated alignframe\r
- for (AlignmentPanel ap : _colourwith)\r
- {\r
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);\r
- }\r
- }\r
- }\r
-\r
- public void chainColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- chainColour.setSelected(true);\r
- jmb.colourByChain();\r
- }\r
-\r
- public void chargeColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- chargeColour.setSelected(true);\r
- jmb.colourByCharge();\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- zappoColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- taylorColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new TaylorColourScheme());\r
- }\r
-\r
- public void hydroColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- hydroColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- helixColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- strandColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- turnColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- buriedColour.setSelected(true);\r
- jmb.setJalviewColourScheme(new BuriedColourScheme());\r
- }\r
-\r
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- setJalviewColourScheme(new PurinePyrimidineColourScheme());\r
- }\r
-\r
- public void userColour_actionPerformed(ActionEvent actionEvent)\r
- {\r
- userColour.setSelected(true);\r
- new UserDefinedColours(this, null);\r
- }\r
-\r
- public void backGround_actionPerformed(ActionEvent actionEvent)\r
- {\r
- java.awt.Color col = JColorChooser.showDialog(this,\r
- "Select Background Colour", null);\r
- if (col != null)\r
- {\r
- jmb.setBackgroundColour(col);\r
- }\r
- }\r
-\r
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)\r
- {\r
- try\r
- {\r
- jalview.util.BrowserLauncher\r
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");\r
- } catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- public void showConsole(boolean showConsole)\r
- {\r
-\r
- if (showConsole)\r
- {\r
- if (splitPane == null)\r
- {\r
- splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);\r
- splitPane.setTopComponent(renderPanel);\r
- splitPane.setBottomComponent(scriptWindow);\r
- this.getContentPane().add(splitPane, BorderLayout.CENTER);\r
- splitPane.setDividerLocation(getHeight() - 200);\r
- scriptWindow.setVisible(true);\r
- scriptWindow.validate();\r
- splitPane.validate();\r
- }\r
-\r
- }\r
- else\r
- {\r
- if (splitPane != null)\r
- {\r
- splitPane.setVisible(false);\r
- }\r
-\r
- splitPane = null;\r
-\r
- this.getContentPane().add(renderPanel, BorderLayout.CENTER);\r
- }\r
-\r
- validate();\r
- }\r
-\r
- class RenderPanel extends JPanel\r
- {\r
- final Dimension currentSize = new Dimension();\r
-\r
- final Rectangle rectClip = new Rectangle();\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- getSize(currentSize);\r
- g.getClipBounds(rectClip);\r
-\r
- if (jmb.fileLoadingError != null)\r
- {\r
- g.setColor(Color.black);\r
- g.fillRect(0, 0, currentSize.width, currentSize.height);\r
- g.setColor(Color.white);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);\r
- StringBuffer sb = new StringBuffer();\r
- int lines = 0;\r
- for (int e = 0; e < jmb.pdbentry.length; e++)\r
- {\r
- sb.append(jmb.pdbentry[e].getId());\r
- if (e < jmb.pdbentry.length - 1)\r
- {\r
- sb.append(",");\r
- }\r
-\r
- if (e == jmb.pdbentry.length - 1 || sb.length() > 20)\r
- {\r
- lines++;\r
- g.drawString(sb.toString(), 20, currentSize.height / 2 - lines\r
- * g.getFontMetrics().getHeight());\r
- }\r
- }\r
- }\r
- else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())\r
- {\r
- g.setColor(Color.black);\r
- g.fillRect(0, 0, currentSize.width, currentSize.height);\r
- g.setColor(Color.white);\r
- g.setFont(new Font("Verdana", Font.BOLD, 14));\r
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);\r
- }\r
- else\r
- {\r
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);\r
- }\r
- }\r
- }\r
-\r
- String viewId = null;\r
-\r
- public String getViewId()\r
- {\r
- if (viewId == null)\r
- {\r
- viewId = System.currentTimeMillis() + "." + this.hashCode();\r
- }\r
- return viewId;\r
- }\r
-\r
- public void updateTitleAndMenus()\r
- {\r
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)\r
- {\r
- repaint();\r
- return;\r
- }\r
- setChainMenuItems(jmb.chainNames);\r
-\r
- this.setTitle(jmb.getViewerTitle());\r
- if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)\r
- {\r
- jmolActionMenu.setVisible(true);\r
- }\r
- if (!jmb.isLoadingFromArchive())\r
- {\r
- seqColour_actionPerformed(null);\r
- }\r
- }\r
-\r
- protected void buildJmolActionMenu()\r
- {\r
- if (_alignwith == null)\r
- {\r
- _alignwith = new Vector<AlignmentPanel>();\r
- }\r
- if (_alignwith.size() == 0 && ap != null)\r
- {\r
- _alignwith.add(ap);\r
- }\r
- ;\r
- for (Component c : jmolActionMenu.getMenuComponents())\r
- {\r
- if (c != alignStructs)\r
- {\r
- jmolActionMenu.remove((JMenuItem) c);\r
- }\r
- }\r
- final ItemListener handler;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see\r
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event\r
- * .ActionEvent)\r
- */\r
- @Override\r
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)\r
- {\r
- alignStructs_withAllAlignPanels();\r
- }\r
-\r
- private void alignStructs_withAllAlignPanels()\r
- {\r
- if (ap == null)\r
- {\r
- return;\r
- }\r
- ;\r
- if (_alignwith.size() == 0)\r
- {\r
- _alignwith.add(ap);\r
- }\r
- ;\r
- try\r
- {\r
- AlignmentI[] als = new Alignment[_alignwith.size()];\r
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];\r
- int[] alm = new int[_alignwith.size()];\r
- int a = 0;\r
-\r
- for (AlignmentPanel ap : _alignwith)\r
- {\r
- als[a] = ap.av.getAlignment();\r
- alm[a] = -1;\r
- alc[a++] = ap.av.getColumnSelection();\r
- }\r
- jmb.superposeStructures(als, alm, alc);\r
- } catch (Exception e)\r
- {\r
- StringBuffer sp = new StringBuffer();\r
- for (AlignmentPanel ap : _alignwith)\r
- {\r
- sp.append("'" + ap.alignFrame.getTitle() + "' ");\r
- }\r
- Cache.log.info("Couldn't align structures with the " + sp.toString()\r
- + "associated alignment panels.", e);\r
-\r
- }\r
-\r
- }\r
-\r
- public void setJalviewColourScheme(ColourSchemeI ucs)\r
- {\r
- jmb.setJalviewColourScheme(ucs);\r
-\r
- }\r
-\r
- /**\r
- * \r
- * @param alignment\r
- * @return first alignment panel displaying given alignment, or the default\r
- * alignment panel\r
- */\r
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)\r
- {\r
- for (AlignmentPanel ap : getAllAlignmentPanels())\r
- {\r
- if (ap.av.getAlignment() == alignment)\r
- {\r
- return ap;\r
- }\r
- }\r
- return ap;\r
- }\r
-\r
- /**\r
- * \r
- * @param ap2\r
- * @return true if this Jmol instance is linked with the given alignPanel\r
- */\r
- public boolean isLinkedWith(AlignmentPanel ap2)\r
- {\r
- return _aps.contains(ap2.av.getSequenceSetId());\r
- }\r
-\r
- public boolean isUsedforaligment(AlignmentPanel ap2)\r
- {\r
-\r
- return (_alignwith != null) && _alignwith.contains(ap2);\r
- }\r
-\r
- public boolean isUsedforcolourby(AlignmentPanel ap2)\r
- {\r
- return (_colourwith != null) && _colourwith.contains(ap2);\r
- }\r
-\r
- /**\r
- * \r
- * @return TRUE if the view is NOT being coloured by sequence associations.\r
- */\r
- public boolean isColouredByJmol()\r
- {\r
- return !jmb.isColourBySequence();\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+public class AppJmol extends StructureViewerBase
+{
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
+
+ private static final String SPACE = " ";
+
+ private static final String BACKSLASH = "\"";
+
+ AppJmolBinding jmb;
+
+ JPanel scriptWindow;
+
+ JSplitPane splitPane;
+
+ RenderPanel renderPanel;
+
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is
+ * handling them
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ */
+ public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
+ AlignmentPanel ap, boolean usetoColour, boolean useToAlign,
+ boolean leaveColouringToJmol, String loadStatus,
+ Rectangle bounds, String viewid)
+ {
+ PDBEntry[] pdbentrys = new PDBEntry[files.length];
+ for (int i = 0; i < pdbentrys.length; i++)
+ {
+ // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+ PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+ files[i]);
+ pdbentrys[i] = pdbentry;
+ }
+ // / TODO: check if protocol is needed to be set, and if chains are
+ // autodiscovered.
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
+
+ jmb.setLoadingFromArchive(true);
+ addAlignmentPanel(ap);
+ if (useToAlign)
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ initMenus();
+ if (leaveColouringToJmol || !usetoColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (usetoColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
+ this.setBounds(bounds);
+ setViewId(viewid);
+ // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+ // bounds.width,bounds.height);
+
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer(false);
+ }
+ });
+ initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+ }
+
+ @Override
+ protected void initMenus()
+ {
+ super.initMenus();
+
+ viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
+
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
+ }
+
+ IProgressIndicator progressBar = null;
+
+ /**
+ * add a single PDB structure to a new or existing Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ final AlignmentPanel ap)
+ {
+ progressBar = ap.alignFrame;
+ String pdbId = pdbentry.getId();
+
+ /*
+ * If the PDB file is already loaded, the user may just choose to add to an
+ * existing viewer (or cancel)
+ */
+ if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
+ {
+ return;
+ }
+
+ /*
+ * Check if there are other Jmol views involving this alignment and prompt
+ * user about adding this molecule to one of them
+ */
+ if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
+ {
+ return;
+ }
+
+ /*
+ * If the options above are declined or do not apply, open a new viewer
+ */
+ openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ }
+
+ private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ progressBar = ap.alignFrame;
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+
+ if (pdbentrys.length > 1)
+ {
+ alignAddedStructures = true;
+ useAlignmentPanelForSuperposition(ap);
+ }
+ jmb.setColourBySequence(true);
+ setSize(400, 400); // probably should be a configurable/dynamic default here
+ initMenus();
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+
+ this.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ {
+ closeViewer(false);
+ }
+ });
+
+ }
+
+ /**
+ * create a new Jmol containing several structures superimposed using the
+ * given alignPanel.
+ *
+ * @param ap
+ * @param pe
+ * @param seqs
+ */
+ public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ {
+ openNewJmol(ap, pe, seqs);
+ }
+
+ /**
+ * Returns a list of any Jmol viewers. The list is restricted to those linked
+ * to the given alignment panel if it is not null.
+ */
+ @Override
+ protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
+ {
+ List<StructureViewerBase> result = new ArrayList<StructureViewerBase>();
+ JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof AppJmol)
+ {
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
+ result.add((StructureViewerBase) frame);
+ }
+ }
+ }
+ return result;
+ }
+
+ void initJmol(String command)
+ {
+ jmb.setFinishedInit(false);
+ renderPanel = new RenderPanel();
+ // TODO: consider waiting until the structure/view is fully loaded before
+ // displaying
+ this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
+ jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+ getBounds().width, getBounds().height);
+ if (scriptWindow == null)
+ {
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
+ }
+
+ jmb.allocateViewer(renderPanel, true, "", null, null, "",
+ scriptWindow, null);
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
+ {
+ command = "";
+ }
+ jmb.evalStateCommand(command);
+ jmb.evalStateCommand("set hoverDelay=0.1");
+ jmb.setFinishedInit(true);
+ }
+
+
+
+ boolean allChainsSelected = false;
+
+ @Override
+ void showSelectedChains()
+ {
+ Vector<String> toshow = new Vector<String>();
+ for (int i = 0; i < chainMenu.getItemCount(); i++)
+ {
+ if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+ if (item.isSelected())
+ {
+ toshow.addElement(item.getText());
+ }
+ }
+ }
+ jmb.centerViewer(toshow);
+ }
+
+ @Override
+ public void closeViewer(boolean closeExternalViewer)
+ {
+ // Jmol does not use an external viewer
+ if (jmb != null)
+ {
+ jmb.closeViewer();
+ }
+ setAlignmentPanel(null);
+ _aps.clear();
+ _alignwith.clear();
+ _colourwith.clear();
+ // TODO: check for memory leaks where instance isn't finalised because jmb
+ // holds a reference to the window
+ jmb = null;
+ }
+
+ @Override
+ public void run()
+ {
+ _started = true;
+ try
+ {
+ List<String> files = fetchPdbFiles();
+ if (files.size() > 0)
+ {
+ showFilesInViewer(files);
+ }
+ } finally
+ {
+ _started = false;
+ worker = null;
+ }
+ }
+
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List<String> files)
+ {
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(BACKSLASH)
+ .append(Platform.escapeString(s)).append(BACKSLASH);
+ }
+ String filesString = fileList.toString();
+
+ if (!addingStructures)
+ {
+ try
+ {
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't open Jmol viewer!", ex);
+ }
+ }
+ else
+ {
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final String command = cmd.toString();
+ lastnotify = jmb.getLoadNotifiesHandled();
+
+ try
+ {
+ jmb.evalStateCommand(command);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Cache.log.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ }
+ }
+
+ // need to wait around until script has finished
+ int waitMax = JMOL_LOAD_TIMEOUT;
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length == files.size()))
+ {
+ try
+ {
+ Cache.log.debug("Waiting around for jmb notify.");
+ Thread.sleep(waitFor);
+ waitTotal += waitFor;
+ } catch (Exception e)
+ {
+ }
+ if (waitTotal > waitMax)
+ {
+ System.err
+ .println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+// System.err.println("finished: " + jmb.isFinishedInit()
+// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+// + "; files: " + files.toString());
+ jmb.getPdbFile();
+ break;
+ }
+ }
+
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ {
+ alignAddedStructures();
+ }
+ addingStructures = false;
+ }
+
+ /**
+ * Queues a thread to align structures with Jalview alignments
+ */
+ void alignAddedStructures()
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (jmb.viewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructs_withAllAlignPanels();
+ }
+ }
+ });
+ alignAddedStructures = false;
+ }
+
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * @return
+ */
+ List<String> fetchPdbFiles()
+ {
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<String>();
+ String pdbid = "";
+ try
+ {
+ String[] filesInViewer = jmb.getPdbFile();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ Pdb pdbclient = new Pdb();
+ for (int pi = 0; pi < jmb.getPdbCount(); pi++)
+ {
+ String file = jmb.getPdbEntry(pi).getFile();
+ if (file == null)
+ {
+ // retrieve the pdb and store it locally
+ AlignmentI pdbseq = null;
+ pdbid = jmb.getPdbEntry(pi).getId();
+ long hdl = pdbid.hashCode() - System.currentTimeMillis();
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_pdb", new String[] { pdbid }), hdl);
+ }
+ try
+ {
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ } finally
+ {
+ if (progressBar != null)
+ {
+ progressBar.setProgressBar(
+ MessageManager.getString("label.state_completed"),
+ hdl);
+ }
+ }
+ if (pdbseq != null)
+ {
+ // just transfer the file name from the first sequence's first
+ // PDBEntry
+ file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
+ .elementAt(0).getFile()).getAbsolutePath();
+ jmb.getPdbEntry(pi).setFile(file);
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ addingStructures = true; // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
+ {
+ if (filesInViewer[c].equals(file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.add(file);
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
+ }
+ if (errormsgs.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[] { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return files;
+ }
+
+ @Override
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+ }
+
+ @Override
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+ }
+
+ void makePDBImage(jalview.util.ImageMaker.TYPE type)
+ {
+ int width = getWidth();
+ int height = getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+ width, height, null, null, null, 0, false);
+ }
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
+ {
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+ width, height, null, this.getTitle(), null, 0, false);
+ }
+ else
+ {
+
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+ width, height, null, this.getTitle(), null, 0, false);
+ }
+
+ if (im.getGraphics() != null)
+ {
+ jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
+ im.writeImage();
+ }
+ }
+
+ @Override
+ public void showHelp_actionPerformed(ActionEvent actionEvent)
+ {
+ try
+ {
+ BrowserLauncher
+ .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void showConsole(boolean showConsole)
+ {
+
+ if (showConsole)
+ {
+ if (splitPane == null)
+ {
+ splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT);
+ splitPane.setTopComponent(renderPanel);
+ splitPane.setBottomComponent(scriptWindow);
+ this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
+ }
+
+ }
+ else
+ {
+ if (splitPane != null)
+ {
+ splitPane.setVisible(false);
+ }
+
+ splitPane = null;
+
+ this.getContentPane().add(renderPanel, BorderLayout.CENTER);
+ }
+
+ validate();
+ }
+
+ class RenderPanel extends JPanel
+ {
+ final Dimension currentSize = new Dimension();
+
+ @Override
+ public void paintComponent(Graphics g)
+ {
+ getSize(currentSize);
+
+ if (jmb != null && jmb.hasFileLoadingError())
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString(MessageManager.getString("label.error_loading_file")
+ + "...", 20, currentSize.height / 2);
+ StringBuffer sb = new StringBuffer();
+ int lines = 0;
+ for (int e = 0; e < jmb.getPdbCount(); e++)
+ {
+ sb.append(jmb.getPdbEntry(e).getId());
+ if (e < jmb.getPdbCount() - 1)
+ {
+ sb.append(",");
+ }
+
+ if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
+ {
+ lines++;
+ g.drawString(sb.toString(), 20, currentSize.height / 2 - lines
+ * g.getFontMetrics().getHeight());
+ }
+ }
+ }
+ else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
+ }
+ else
+ {
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
+ }
+ }
+ }
+
+ @Override
+ public AAStructureBindingModel getBinding()
+ {
+ return this.jmb;
+ }
+
+ @Override
+ public String getStateInfo()
+ {
+ return jmb == null ? null : jmb.viewer.getStateInfo();
+ }
+
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
+ @Override
+ protected String getViewerName()
+ {
+ return "Jmol";
+ }
+}
git://source.jalview.org / jalview.git / blobdiff